User: Laven9

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Laven90
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Posts by Laven9

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Strange plots I got from R studio
... Recently, when I plot by R, all the plots I got have no X axis and Y axis, by default. It just happened suddenly and I really need helps. I was following "seraut": plot1 <- FeatureScatter(pbmc, feature1 = "nCount_RNA", feature2 = "percent.mt") And I got my plot with no axis. As ...
R written 1 day ago by Laven90
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How to interpret ABSOLUTE output?
... There are multiple headers in ABSOLUTE output *ABS_MAF.txt. How should I interpret them? Or in what situation should I infer a mutation is clonal/subclonal? I could find out some sayings of part of headers ,like "*Pr_somatic_clonal*: probability that SNV is somatic and strictly clonal" Maybe, but o ...
absolute written 12 months ago by Laven90
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ERROR running annovar with cosmic90
... I am trying to run annovar with cosmic90. When preparing files, I follow the command: prepare_annovar_user.pl -dbtype cosmic .CosmicMutantExport.tsv -vcf CosmicCodingMuts.vcf > hg38_cosmic90_coding.txt But it went wrong, with error:`COSMIC MutantExport format error: column 17 or 12 should b ...
annovar cosmic written 12 months ago by Laven90 • updated 11 months ago by supriya.awasthy10
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(Closed) How to download faster in Linux?
... I am trying to download a 11G file. I use commands like: aria2c -x5 -c --the link--. It seems it is slow to do so , as the DL shows only 100-180k. And it would take me almost 25h to complete the downloading. It is acceptable. But I am wondering if there are some other faster methods I could try? I t ...
linux written 12 months ago by Laven90
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Comment: A: A question on GetPileupSummaries (GATK)
... Thank you, MatthewP ! But as I am new in the field, could you please tell me how to interpret the file common_all_xxx.vcf.gz? If it is right that in my opinion, it should be a file containing all the common snps in a large group of people, so that gatk4 could use it to exclude those snps in the Mut ...
written 12 months ago by Laven90
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A question on GetPileupSummaries (GATK)
... I am confusing what "common_biallelic.vcf.gz" is? Am I right if I run it like this: gatk SelectVariants \ -R Homo_sapiens_assembly38.fasta \ -V gnomad.vcf.gz \ --restrict-alleles-to biallelic \ -O common_biallelic.vcf.gz Or should I change the -V for something else like my ...
getpileupsummaries written 12 months ago by Laven90
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Comment: A: A question on GenomicsDBImport (GATK)
... Thank you, Pierre and Nicolas! It do help me a lot! ...
written 13 months ago by Laven90
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Comment: A: A question on GenomicsDBImport (GATK)
... I still have questions: 1) If it is better if I used the .Bed file the company offered than "wgs_calling_regions.hg38.interval_list"? 2) Once I split the .Bed file into smaller ones, it would create multiple "gendb://GDB "(s). How can I imerge them to run the "CreateSomaticPanelOfNormals"? Can simpl ...
written 13 months ago by Laven90 • updated 13 months ago by genomax91k
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A question on GenomicsDBImport (GATK)
... I am now trying to use GenomicsDBImport (GATK). I have a .bed file for my WES sequencing. Should I split the .bed file into small .bed files in order to make it fast (it is much faster if only <=100 intervals is given) or should I run each chromosome every time to produce a complete GVCFs? ...
genomicsdbimport written 13 months ago by Laven90
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(Closed) How to make a new /tmp/ file?
... I am a non-root user for linux. And I want to make a new /tmp/ in my /home/. But how to make it default? And can I limit its biggest size without root right? ...
tmp linux written 14 months ago by Laven90

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